Structure of PDB 6uml Chain C Binding Site BS03

Receptor Information
>6uml Chain C (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFDTSLPTSHTYLFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFH
PQEVSMVRNLIQKDRTFAVLYSEAQFGTTAEIYAYREEQDFGIEIVKVKA
IGRQRFKQAKVQILPECVLPSTMSAVQLESLNKCQIFSYKWWQKYQKRKF
HCANLTSWPRWLYSLYDAETLMDRIKKQLREWDLPSNPIDFSYRVAACLP
IDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFS
LSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVA
QCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIP
Ligand information
Ligand IDY70
InChIInChI=1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)/t8-/m0/s1
InChIKeyUVSMNLNDYGZFPF-QMMMGPOBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1NC(=O)CCC1N3C(=O)c2cccc(c2C3=O)N
CACTVS 3.385Nc1cccc2C(=O)N([C@H]3CCC(=O)NC3=O)C(=O)c12
OpenEye OEToolkits 1.9.2c1cc2c(c(c1)N)C(=O)N(C2=O)[C@H]3CCC(=O)NC3=O
CACTVS 3.385Nc1cccc2C(=O)N([CH]3CCC(=O)NC3=O)C(=O)c12
OpenEye OEToolkits 1.9.2c1cc2c(c(c1)N)C(=O)N(C2=O)C3CCC(=O)NC3=O
FormulaC13 H11 N3 O4
NameS-Pomalidomide
ChEMBLCHEMBL2093113
DrugBank
ZINCZINC000003940470
PDB chain6uml Chain C Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6uml Crystal structure of the SALL4-pomalidomide-cereblon-DDB1 complex.
Resolution3.58 Å
Binding residue
(original residue number in PDB)		N351 P352 H353 H378 W380 W386 W400 F402
Binding residue
(residue number reindexed from 1)		N262 P263 H264 H289 W291 W297 W311 F313
Annotation score1
Binding affinityBindingDB: IC50=2000nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0044325 transmembrane transporter binding
GO:0046872 metal ion binding
Biological Process
GO:0016567 protein ubiquitination
GO:0030177 positive regulation of Wnt signaling pathway
GO:0031333 negative regulation of protein-containing complex assembly
GO:0031334 positive regulation of protein-containing complex assembly
GO:0034766 negative regulation of monoatomic ion transmembrane transport
GO:0035641 locomotory exploration behavior
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:1902607 negative regulation of large conductance calcium-activated potassium channel activity
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6uml, PDBe:6uml, PDBj:6uml
PDBsum6uml
PubMed32251415
UniProtQ96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)

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